Increase in global ship transport induces building of Ultra Large Container Ships (ULCS), which have a capacity up to 14000 TEU with length up to 400 m, without changes of the operational requirements (speed around 27 knots). Natural frequencies of such ships can fall into the range of encounter frequencies in an ordinary sea spectrum. Present Classification Rules for ship design and construction don't cover such conditions completely and hydroelastic analysis of ULCS seems to be the appropriate solution for analysis of their response in waves. This paper deals with numerical procedure for ship hydroelastic analysis with particular emphasis on improvements of the present beam structural model. The structural model represents a constitutive part of hydroelastic mathematical model and generally it can be formulated either as 1D FEM or 3D FEM model. For the preliminary design stage hydroelastic model derived by coupling 1D FEM structural model and 3D BEM hydrodynamic one seems to be an appropriate choice. Within the paper the importance of hydroelastic approach and methodology of hydroelastic analysis are elaborated. Further on, structural model based on advanced beam theory is described in details. The improvements include taking into account shear influence on torsion, contribution of bulkheads to hull stiffness as well as determination of effective stiffness of engine room structure. Along with that, hydrodynamic and hydrostatic models are presented in a condensed form. Numerical example, which includes complete hydroelastic analysis of a large container ship, is also added. In this case, validation of 1D FEM model is checked by correlation analysis with the vibration response of the fine 3D FEM model. The procedure related to determination of engine room effective stiffness is checked by 3D FEM analysis of ship-like pontoon which has been made according to the considered ship characteristics.